chr2-10432727-A-C

Variant names:

• chr2-10432727-A-C
• rs13000916
• ENST00000757688.1:n.176T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000757688.1(ENSG00000298739):​n.176T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,104 control chromosomes in the GnomAD database, including 34,072 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (34072 hom., cov: 34)
• Consequence: ENSG00000298739 ENST00000757688.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 4 publications found

Genes affected

ENSG00000298739 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907732	XR_007086214.1	n.87T>G		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124907732	XR_007086213.1	n.-119T>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298739	ENST00000757688.1	n.176T>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000298739	ENST00000757689.1	n.119T>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000298698	ENST00000757451.1	n.251+483A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98755 AN: 151986 Hom.: 34025 Cov.: 34

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.589

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.650 AC: 98858 AN: 152104 Hom.: 34072 Cov.: 34 AF XY: 0.651 AC XY: 48420 AN XY: 74358

African (AFR) AF: 0.886 AC: 36778 AN: 41526

American (AMR) AF: 0.460 AC: 7037 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3468

East Asian (EAS) AF: 0.436 AC: 2236 AN: 5126

South Asian (SAS) AF: 0.610 AC: 2942 AN: 4822

European-Finnish (FIN) AF: 0.716 AC: 7593 AN: 10600

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38639 AN: 67954

Other (OTH) AF: 0.592 AC: 1251 AN: 2114

Alfa AF: 0.493 Hom.: 1353

Bravo AF: 0.635

Asia WGS AF: 0.538 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.70
PhyloP100		-2.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13000916; hg19: chr2-10572853;